Nuclear RNA synthesis is repressed during the mitotic phase of each cell cycle. Although total RNA synthesis remains low throughout mitosis, the degree of RNA polymerase II transcription repression on specific genes has not been examined. In addition, it is not known whether mitotic repression of RNA polymerase II transcription is due to polymerase pausing or ejection of transcription elongation complexes from mitotic chromosomes. In this study, we show that RNA polymerase II transcription is repressed in mammalian cells on a number of specific gene regions during mitosis. We also show that the majority of RNA polymerase II transcription elongation complexes are physically excluded from mitotic chromosomes between late prophase and late telophase. Despite generalized transcription repression and stripping of RNA polymerase II complexes from DNA, arrested RNA polymerase II ternary complexes appear to remain on some gene regions during mitosis. The cyclic repression of transcription and ejection of RNA polymerase II transcription elongation complexes may help regulate the transcriptional events that control cell cycle progression and differentiation.In higher eukaryotes, mitosis is accompanied by dramatic and reversible transformations to the structural organization of both cytoplasm and nucleus (reviewed in references 12, 28, 39, and 40). Mitosis is also accompanied by profound biochemical changes, including a decline in nuclear RNA synthesis. Mitotic repression of transcription was first noted over 30 years ago, in studies analyzing incorporation of RNA precursors during the cell cycle (22,29,44,68,69). In these studies, it was observed that incorporation of radioactive precursors into nuclear RNA declines in early to mid-prophase and resumes in late telophase. The precise degree of mitotic transcription repression remains uncertain, with some studies detecting mitotic RNA synthesis at 16 to 24% of interphase levels (22,27,29,80). In addition, it is not clear to what degree transcription by each of the three nuclear RNA polymerases (RNAPs) is repressed during mitosis. As approximately 75 to 80% of RNA synthesis in cycling cells is due to RNAP I activity (32,46,77), it is possible that some RNAP I, II, or III transcription may escape mitotic repression but be undetectable by pulse-labeling. In addition, pulse-labeling assays measure steady-state RNA levels, which arise through a combination of RNA synthesis and degradation. Therefore, it is possible that part of the loss of labeled steady-state RNA in mitotic cells is due to degradation of nascent labeled RNAs.Although mitotic repression of RNAP I and III activity has been examined in some detail in the last few years (16,19,23,51,54,72,73), few studies of RNAP II transcription during mitosis have been reported. The in situ hybridization studies of Shermoen and O'Farrell (59) demonstrate that nascent transcripts from the Drosophila RNAP II-transcribed gene Ubx are aborted and degraded during mitosis. These data suggest that RNAP II transcription complexes may be ...